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14375 Commits

Author SHA1 Message Date
Steven J. Plimpton 0c4c002f34 patch 8Mar18 2018-03-08 08:19:46 -07:00
Steve Plimpton bad1cdde78
Merge pull request #831 from lammps/mpi4py-version 
allow for mpi4py version 2 or 3 in Python wrapper
 2018-03-07 14:01:22 -07:00
Steve Plimpton 626ca25d05
Merge pull request #830 from akohlmey/more-fixes-for-stable 
More small fixes for stable release
 2018-03-07 14:00:32 -07:00
Axel Kohlmeyer a1bb877d55 correct commented out MPI examples 2018-03-07 11:17:03 -05:00
Axel Kohlmeyer 63c0a35fab remove code that has no effect 2018-03-07 11:12:08 -05:00
Axel Kohlmeyer 812572ea97 update dependencies for colvars library 2018-03-07 10:57:56 -05:00
Axel Kohlmeyer f91c36878c remove dead code 2018-03-07 10:57:07 -05:00
Steven J. Plimpton fd1edaf04f allow for mpi4py version 2 or 3 in Python wrapper 2018-03-07 08:52:46 -07:00
Axel Kohlmeyer 47e2ca6eb2 apply bugfix to reaxff taper function as described in issue #828 2018-03-07 09:52:14 -05:00
Steve Plimpton 8d6fbd9829
Merge pull request #829 from lammps/restartinfo 
add restartinfo=0 to manbody file it was missing from
 2018-03-06 15:17:05 -07:00
Steven J. Plimpton 070e85b44b add restartinfo=0 to manbody file it was missing from 2018-03-06 12:45:40 -07:00
Steve Plimpton 3e535633e6
Merge pull request #827 from akohlmey/fixes-for-stable 
Fixes for stable release
 2018-03-06 12:33:33 -07:00
Axel Kohlmeyer 64779eb576 documentation update for MEAM to clarify the I,J,K indices in the MEAM parameter file 2018-03-06 13:21:34 -05:00
Axel Kohlmeyer 1ca928b331 dead code removal 2018-03-05 20:33:19 -05:00
Axel Kohlmeyer a1bdea1dd8 avoid division by zero for pair styles meam and meam/c 2018-03-05 14:03:10 -05:00
Axel Kohlmeyer 49aad1d157
rename noextra flag to nofix 2018-03-04 09:56:22 -05:00
Axel Kohlmeyer 04bd268745
rename noextra flag to nofix 2018-03-04 09:55:44 -05:00
Axel Kohlmeyer 959883ad03
rename noextra option to nofix 
since this corresponds to the `fix` option of `read_data`, calling this flag `nofix` seems more consistent and descriptive.
 2018-03-04 09:49:50 -05:00
Axel Kohlmeyer 52446eed6d make fix bond/react example inputs more similar to other input examples in LAMMPS 2018-03-03 19:34:31 -05:00
Axel Kohlmeyer e8eeb52636 fix memory leaks detected by valgrind 2018-03-03 19:31:53 -05:00
jrgissing a323147819 noextra option for write_data 2018-03-03 14:28:35 -07:00
Jacob Gissinger 89de70ff32
Merge pull request #4 from lammps/master 
rebase
 2018-03-03 14:17:56 -07:00
Steve Plimpton 45555b017d
Merge pull request #728 from danicholson/cluster-fragment-aggregate-fixes 
Cluster/fragment/aggregate bugfixes
 2018-03-02 15:52:26 -07:00
Steve Plimpton 54f58faab5
Merge pull request #822 from andeplane/gcmc_mpi_error 
Added error if gcmc is used with molecules on more than one processor
 2018-03-02 14:41:03 -07:00
Steve Plimpton 22b6764304
Merge pull request #819 from stanmoore1/package_installed 
Add make package-installed command
 2018-03-02 14:40:36 -07:00
Steve Plimpton 39a09d3a54
Merge pull request #814 from stanmoore1/kk_snap_workaround 
Workaround issue in pair_snap_kokkos
 2018-03-02 14:40:20 -07:00
Steve Plimpton 812a45451a
Merge pull request #816 from giacomofiorin/colvars-update-2018-02-23 
Collected fixes and updates to Colvars library
 2018-03-02 13:15:56 -07:00
Steve Plimpton 0666607ceb
Merge pull request #815 from akohlmey/collected-small-fixes 
Collected small cleanups, fixes, and enhancements
 2018-03-02 13:15:35 -07:00
Anders Hafreager d18ba3b188 Added error if gcmc is used with molecules on more than one processor 2018-03-02 11:23:34 -08:00
Axel Kohlmeyer b1d3b56a17 apply bugfix reported in issue #820 2018-03-02 04:33:13 -05:00
jrgissing 21364f38b0 gatherv fix, take 2 2018-03-01 23:11:46 -07:00
Stan Moore 8d0fdb17a6 Add make package-installed command 2018-03-01 10:39:06 -07:00
Axel Kohlmeyer eadac15466 avoid multiple calls to delete [] on the same pointer. 
thanks to @ExHP for pointing out this issue
 2018-02-28 14:02:16 +01:00
Axel Kohlmeyer 51b19dfd1a plug memory leak in fix bond/react 2018-02-25 14:10:28 +01:00
Axel Kohlmeyer 58e01a9eee plug memory leak in pair style lj/class2/coul/long with coulomb tables 2018-02-25 14:03:07 +01:00
Jacob Gissinger 3b90f60064
Merge pull request #3 from lammps/master 
rebase
 2018-02-24 23:49:27 -07:00
jrgissing 7d1de34533 gatherv fix, doc updates 2018-02-24 22:49:28 -07:00
Axel Kohlmeyer 5fb2979da7 allow dynamic groups for some standard walls interacting with point particles 2018-02-24 13:50:42 -05:00
Axel Kohlmeyer 948f4783aa ring communication *is* called with outbut set to NULL, so don't error out on that. 2018-02-24 17:17:45 +01:00
Axel Kohlmeyer fb6e7e8aea add sanity checks for ring communication 
we do not call memcpy() unless nbytes != 0 and source/target pointer is not NULL
we error out on illegal combinations of nbytes and inbuf/outbuf
 2018-02-24 16:41:10 +01:00
Axel Kohlmeyer bba4bd1489 support offsets for molecule IDs (if available) in read_data similar to atomIDs 
suggested by felipe perez in https://sourceforge.net/p/lammps/mailman/message/36236631/
 2018-02-23 18:02:05 -05:00
Stan Moore 4a875dc67d Workaround for compiler bug in gcc v4.9.3, manifest in KOKKOS SNAP 2018-02-23 09:01:34 -07:00
Giacomo Fiorin f3cf407a21 Collected fixes and updates to Colvars library 
This commit includes several fixes to moving restraints; also added is support
for runtime integration of 2D and 3D PMFs from ABF.

Mostly changes to existing member functions, with few additions in classes not
directly accessible by LAMMPS.  Also removed are calls to std::pow(), replaced
by a copy of MathSpecial::powint().

Relevant commits in Colvars repository:

7307b5c 2017-12-14 Doc improvements [Giacomo Fiorin]
7f86f37 2017-12-14 Allow K-changing restraints computing accumulated work; fix staged-k TI estimator [Giacomo Fiorin]
7c1c175 2017-12-14 Fix 1D ABF trying to do pABF [Jérôme Hénin]
b94aa7e 2017-11-16 Unify PMF output for 1D, 2D and 3D in ABF [Jérôme Hénin]
771a88f 2017-11-15 Poisson integration for all BC in 2d and 3d [Jérôme Hénin]
6af4d60 2017-12-01 Print message when issuing cv delete in VMD [Giacomo Fiorin]
4413972 2017-11-30 Check for homogeneous colvar to set it periodic [Jérôme Hénin]
95fe4b2 2017-11-06 Allow abf_integrate to start in bin with 1 sample [Jérôme Hénin]
06eea27 2017-10-23 Shorten a few constructs by using the power function [Giacomo Fiorin]
3165dfb 2017-10-20 Move includes of colvarproxy.h from headers to files [Giacomo Fiorin]
32a867b 2017-10-20 Add optimized powint function from LAMMPS headers [Giacomo Fiorin]
3ad070a 2017-10-20 Remove some unused includes, isolate calls to std::pow() [Giacomo Fiorin]
0aaf540 2017-10-20 Replace all calls to std::pow() where the exponent is not an integer [Giacomo Fiorin]
 2018-02-23 08:34:53 -05:00
Axel Kohlmeyer 0003bb6766 merge capture regions, so the library interface code can compiled with exceptions 2018-02-23 14:20:39 +01:00
Axel Kohlmeyer 523978b4c7 dead code and uninitialized variables detected by clang 2018-02-23 12:04:15 +01:00
Axel Kohlmeyer d5e43a9ab1 whitespace cleanup and reindent 2018-02-23 10:20:29 +01:00
Stan Moore 939b1b2d05 Workaround issue in pair_snap_kokkos_impl 2018-02-22 14:27:23 -07:00
Steve Plimpton 77efd3dfb3
Merge pull request #813 from akohlmey/correct-neighbor-build 
Make default argument for virtual method Neighbor::build() explicit
 2018-02-22 08:48:06 -07:00
Steve Plimpton feb9f29fad
Merge pull request #812 from akohlmey/correct-integrate-setup 
Make default argument for pure method Integrate::setup() explicit
 2018-02-22 08:47:45 -07:00
Steven J. Plimpton bfdf464ee3 patch 22Feb18 2018-02-22 08:46:03 -07:00